World number two Murray is seeded second but Nadal's case was less clear-cut, with John McEnroe among those who claimed he should be moved up from fifth in the rankings to fourth for the grass-court grand slam.
Wimbledon announced, however, that two-time former champion Nadal would be the fifth seed behind his Spanish compatriot David Ferrer, who has inched ahead of him on the ATP rankings.
Murray has lost all three matches to Nadal at Wimbledon
That decision comes after Nadal thrashed Ferrer in straight-sets for his record eighth French Open title earlier this month.
Murray, who won at Queen's Club for a third time on Sunday, has lost to Nadal three times at SW19.
The Spaniard defeated Murray in the 2008 quarter finals as well as in the 2010 and 2011 semi-finals.
Novak Djokovic is top seed, and the Serb and his 2012 conqueror Roger Federer will be keen to avoid the Spaniard in the last eight when the draw is made on Friday.